Locus 1130

Sequence ID 3R_DroMel_CAF1
Location 3,393,580 – 3,393,847
Length 267
Max. P 0.991340
window1854 window1855 window1856

overview

Window 4

Location 3,393,580 – 3,393,697
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.90
Mean single sequence MFE -22.11
Consensus MFE -17.25
Energy contribution -17.75
Covariance contribution 0.50
Combinations/Pair 1.12
Mean z-score -1.42
Structure conservation index 0.78
SVM decision value 0.02
SVM RNA-class probability 0.545837
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3393580 117 - 27905053
CAAAGUUUGUCCAUUGUCUUUUUCUCAUUGUUGAGUAAAAAGUUUGCACUCUUAUUCAGCAGCCAGAUAAACUCAAAUCCAAUUGGCAACAGCUAUGAAUAACAUUUCAUGUAGACC---
........(((..(((..(((.(((..(((((((((((..(((....))).)))))))))))..))).)))..)))......(((....))).((((((......))))))..))).--- ( -21.70)
>DroSim_CAF1 2496 117 - 1
CAAAGUUUGUCCAUUGUCUUUUUCUCAUUGUUGAGUAAAAAGUUUGCACUCUCAUUCAGCAGCCAGAUAAACUCAAAUCCAAUUGGCAACAGCUAUGAAUAACAUUUCAUGUAGACC---
...((((((((......((((((((((....)))).)))))).((((...........))))...)))))))).........(((....))).((((((......))))))......--- ( -21.20)
>DroEre_CAF1 653 120 - 1
CAAAGUUUGCCCAUUGUCUUUUUGUCGUUGCUGAGUAAAAACUUUGCACUCUCAUUCAGCAGCCAGAUAAACUCAAAUCCAAUUGGCAACAGCUAUGAAUAACAUUUCAUUUAGACCUUG
...((((((((.((((..((((((((((((((((((.................))))))))))..)))))....)))..)))).)))))..)))(((((......))))).......... ( -25.93)
>DroYak_CAF1 6178 103 - 1
CAAAGUUUGCCCAUUGUCUUUUUGCCAUUGUUGAGUGAAAACUUUGCACUCUCAUUCAGUAGCCAGAUAAACUCUAAUCCAAUUGGCAACAGCUAUGAAUAAC-----------------
((.((((((((.((((.......((.((((..(((((.........))))).....)))).)).(((.....)))....)))).)))))..))).))......----------------- ( -19.60)
>consensus
CAAAGUUUGCCCAUUGUCUUUUUCUCAUUGUUGAGUAAAAACUUUGCACUCUCAUUCAGCAGCCAGAUAAACUCAAAUCCAAUUGGCAACAGCUAUGAAUAACAUUUCAUGUAGACC___
((.((((((((.((((..((((((((.(((((((((((.............)))))))))))...))))))....))..)))).)))))..))).))....................... (-17.25 = -17.75 +   0.50)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,393,697 – 3,393,816
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.10
Mean single sequence MFE -28.04
Consensus MFE -25.80
Energy contribution -25.55
Covariance contribution -0.25
Combinations/Pair 1.04
Mean z-score -2.25
Structure conservation index 0.92
SVM decision value 1.66
SVM RNA-class probability 0.970351
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3393697 119 + 27905053
UUAUUUCUGGUU-UUUCUGCCACGGGAAUUGUAACGAAACCAUACCAAACGCGGAAAGCAAAAAGAAAGAUAUUGGUCAAGCAACUAAUAAAACUUUCUGUGGCAUUCAAAAAGCGUAUA
.......(((((-((..(((..........)))..)))))))......((((.(((.((....((((((.(((((((......)))))))...))))))...)).))).....))))... ( -25.60)
>DroSim_CAF1 2613 119 + 1
UUAUUUCUGGUU-UUUCUGCCACGGGAAUUGUAACGAAACCAAACCAAACGCGGAAAGCAAAAAGAAAGAUAUUGGUCAAGCAACUAAUAAAACUUUCUGUGGCAUUCAAAAAGCGUAUA
.......(((((-((..(((..........)))..)))))))......((((.(((.((....((((((.(((((((......)))))))...))))))...)).))).....))))... ( -25.80)
>DroEre_CAF1 773 114 + 1
UUAUUUCUGGUU-UUUGUGCCACGGGAAUUGUAAGGAAAC-----CAAACGCGGGAAGCAAAAAGAAAGGUAUUGGUCAAGCAACUAAUAAAACUUUCUGUGGCAUUCAAAAAGCGUAUA
.......(((((-((..(((..........)))..)))))-----)).((((..(((((....((((((.(((((((......)))))))...))))))...)).))).....))))... ( -29.80)
>DroYak_CAF1 6281 115 + 1
UUAUUUCUGGUUUUUUGUGCCACGGGAAUAGUAACGAAAC-----CAAACGCGGGAAGCAAAAAGAAAGGUAUUGGUCAAGCAACUAAUAAAACUUUCUGUGGCAUUCAAAAAGCGUAUA
.........((((((((((((((((..............)-----)....((.....))....((((((.(((((((......)))))))...))))))))))))..))))))))..... ( -30.94)
>consensus
UUAUUUCUGGUU_UUUCUGCCACGGGAAUUGUAACGAAAC_____CAAACGCGGAAAGCAAAAAGAAAGAUAUUGGUCAAGCAACUAAUAAAACUUUCUGUGGCAUUCAAAAAGCGUAUA
...(..(((((.......)))).)..).....................((((.(((.((....((((((.(((((((......)))))))...))))))...)).))).....))))... (-25.80 = -25.55 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,393,736 – 3,393,847
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.36
Mean single sequence MFE -24.88
Consensus MFE -22.39
Energy contribution -21.70
Covariance contribution -0.69
Combinations/Pair 1.10
Mean z-score -2.57
Structure conservation index 0.90
SVM decision value 2.26
SVM RNA-class probability 0.991340
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3393736 111 + 27905053
CAUACCAAACGCGGAAAGCAAAAAGAAAGAUAUUGGUCAAGCAACUAAUAAAACUUUCUGUGGCAUUCAAAAAGCGUAUAGCACUGAAUUCUGUUUUCACCUGA-----AAAAA-AA---
........((((.(((.((....((((((.(((((((......)))))))...))))))...)).))).....))))................(((((....))-----)))..-..--- ( -21.30)
>DroSim_CAF1 2652 116 + 1
CAAACCAAACGCGGAAAGCAAAAAGAAAGAUAUUGGUCAAGCAACUAAUAAAACUUUCUGUGGCAUUCAAAAAGCGUAUAGCACUGAAUCCUGUUUUCACCUGGAUGCCAAAAA-AA---
..........((.....))....((((((.(((((((......)))))))...)))))).(((((((((....((.....))..((((.......))))..)))))))))....-..--- ( -26.70)
>DroEre_CAF1 812 115 + 1
-----CAAACGCGGGAAGCAAAAAGAAAGGUAUUGGUCAAGCAACUAAUAAAACUUUCUGUGGCAUUCAAAAAGCGUAUAGUAGUGAAUCCUGUUUUCACCUGGUUACCAAAAAAAAAAG
-----...((((..(((((....((((((.(((((((......)))))))...))))))...)).))).....))))......(((((.......))))).(((...))).......... ( -25.30)
>DroYak_CAF1 6321 112 + 1
-----CAAACGCGGGAAGCAAAAAGAAAGGUAUUGGUCAAGCAACUAAUAAAACUUUCUGUGGCAUUCAAAAAGCGUAUAGUACUGAAUCCUGUUUUCACCUGGUUCCCAAAAAAAA---
-----.......(((((.((...((((((.(((((((......)))))))...))))))..((.(((((....((.....))..)))))))..........)).)))))........--- ( -26.20)
>consensus
_____CAAACGCGGAAAGCAAAAAGAAAGAUAUUGGUCAAGCAACUAAUAAAACUUUCUGUGGCAUUCAAAAAGCGUAUAGCACUGAAUCCUGUUUUCACCUGGUU_CCAAAAA_AA___
..........(..(((((((...((((((.(((((((......)))))))...))))))..((.(((((....((.....))..))))))))))))))..)................... (-22.39 = -21.70 +  -0.69)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:46 2006